Starting phenix.real_space_refine on Wed Jun 3 14:52:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxc_64580/06_2026/9uxc_64580_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxc_64580/06_2026/9uxc_64580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uxc_64580/06_2026/9uxc_64580_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxc_64580/06_2026/9uxc_64580_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uxc_64580/06_2026/9uxc_64580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxc_64580/06_2026/9uxc_64580.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 4040 2.51 5 N 1089 2.21 5 O 1220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6400 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 425 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain: "B" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2541 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 17, 'TRANS': 308} Chain breaks: 1 Chain: "C" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3182 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 22, 'TRANS': 387} Chain breaks: 1 Chain: "D" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 192 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.86, per 1000 atoms: 0.29 Number of scatterers: 6400 At special positions: 0 Unit cell: (75.19, 88.33, 108.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 5 15.00 Mg 2 11.99 O 1220 8.00 N 1089 7.00 C 4040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 484.7 milliseconds 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1502 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 47.9% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 462 through 510 removed outlier: 3.680A pdb=" N ARG A 466 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 92 Processing helix chain 'B' and resid 112 through 125 removed outlier: 4.100A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.717A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.638A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 254 Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.802A pdb=" N LEU B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 removed outlier: 3.507A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 348 through 349 No H-bonds generated for 'chain 'B' and resid 348 through 349' Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.679A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.533A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 111 removed outlier: 3.620A pdb=" N PHE C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 119 removed outlier: 3.539A pdb=" N LEU C 118 " --> pdb=" O GLU C 115 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS C 119 " --> pdb=" O ALA C 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 115 through 119' Processing helix chain 'C' and resid 130 through 144 Processing helix chain 'C' and resid 155 through 163 removed outlier: 3.524A pdb=" N ASN C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 193 removed outlier: 3.570A pdb=" N ILE C 193 " --> pdb=" O GLN C 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 190 through 193' Processing helix chain 'C' and resid 199 through 214 Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 248 through 268 removed outlier: 4.021A pdb=" N ASP C 262 " --> pdb=" O CYS C 258 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C 263 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 299 through 305 removed outlier: 3.771A pdb=" N ARG C 302 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 311 removed outlier: 3.958A pdb=" N PHE C 310 " --> pdb=" O PRO C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 315 removed outlier: 3.586A pdb=" N VAL C 315 " --> pdb=" O PRO C 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 312 through 315' Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.578A pdb=" N MET C 336 " --> pdb=" O THR C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 348 removed outlier: 3.618A pdb=" N SER C 348 " --> pdb=" O GLY C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 372 removed outlier: 3.547A pdb=" N ARG C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 392 Processing helix chain 'C' and resid 392 through 403 Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.612A pdb=" N GLU C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 429 Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 32 removed outlier: 3.515A pdb=" N PHE B 31 " --> pdb=" O CYS B 17 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA3, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.051A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N MET B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 238 through 240 Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 39 removed outlier: 4.202A pdb=" N PHE C 38 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU C 15 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N SER C 124 " --> pdb=" O LEU C 15 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N PHE C 17 " --> pdb=" O SER C 124 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 45 removed outlier: 3.819A pdb=" N TYR C 70 " --> pdb=" O GLY C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 90 Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 188 removed outlier: 3.641A pdb=" N VAL C 194 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 187 through 188 removed outlier: 7.138A pdb=" N ILE C 350 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 169 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA C 352 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU C 171 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 349 " --> pdb=" O ILE C 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 224 through 227 removed outlier: 4.307A pdb=" N SER C 226 " --> pdb=" O LYS C 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 286 through 290 removed outlier: 6.703A pdb=" N PHE C 290 " --> pdb=" O TYR C 294 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 32 through 38 288 hydrogen bonds defined for protein. 783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1695 1.33 - 1.45: 1167 1.45 - 1.57: 3599 1.57 - 1.69: 8 1.69 - 1.81: 73 Bond restraints: 6542 Sorted by residual: bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C5 ADP B 501 " pdb=" C6 ADP B 501 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" N ILE C 71 " pdb=" CA ILE C 71 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.14e-02 7.69e+03 1.15e+01 bond pdb=" CA SER B 33 " pdb=" CB SER B 33 " ideal model delta sigma weight residual 1.524 1.481 0.042 1.33e-02 5.65e+03 1.01e+01 bond pdb=" N VAL C 45 " pdb=" CA VAL C 45 " ideal model delta sigma weight residual 1.460 1.504 -0.044 1.42e-02 4.96e+03 9.73e+00 ... (remaining 6537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 8632 2.31 - 4.63: 189 4.63 - 6.94: 37 6.94 - 9.25: 8 9.25 - 11.56: 5 Bond angle restraints: 8871 Sorted by residual: angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 126.61 10.22 1.00e+00 1.00e+00 1.04e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 130.14 9.73 1.00e+00 1.00e+00 9.47e+01 angle pdb=" C THR B 304 " pdb=" N MET B 305 " pdb=" CA MET B 305 " ideal model delta sigma weight residual 122.56 112.93 9.63 1.72e+00 3.38e-01 3.13e+01 angle pdb=" C PRO D 51 " pdb=" CA PRO D 51 " pdb=" CB PRO D 51 " ideal model delta sigma weight residual 111.39 105.27 6.12 1.28e+00 6.10e-01 2.29e+01 angle pdb=" CA SER B 33 " pdb=" C SER B 33 " pdb=" O SER B 33 " ideal model delta sigma weight residual 122.37 117.82 4.55 1.15e+00 7.56e-01 1.56e+01 ... (remaining 8866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.39: 3701 29.39 - 58.78: 205 58.78 - 88.17: 33 88.17 - 117.55: 2 117.55 - 146.94: 1 Dihedral angle restraints: 3942 sinusoidal: 1607 harmonic: 2335 Sorted by residual: dihedral pdb=" C5' ADP B 501 " pdb=" O5' ADP B 501 " pdb=" PA ADP B 501 " pdb=" O2A ADP B 501 " ideal model delta sinusoidal sigma weight residual 300.00 153.06 146.94 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" O1B ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PB ADP B 501 " pdb=" PA ADP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 -166.10 106.10 1 2.00e+01 2.50e-03 3.07e+01 dihedral pdb=" CG ARG B 372 " pdb=" CD ARG B 372 " pdb=" NE ARG B 372 " pdb=" CZ ARG B 372 " ideal model delta sinusoidal sigma weight residual 180.00 135.16 44.84 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 3939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 752 0.054 - 0.107: 193 0.107 - 0.161: 30 0.161 - 0.215: 4 0.215 - 0.268: 1 Chirality restraints: 980 Sorted by residual: chirality pdb=" CA LEU C 76 " pdb=" N LEU C 76 " pdb=" C LEU C 76 " pdb=" CB LEU C 76 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE D 46 " pdb=" N ILE D 46 " pdb=" C ILE D 46 " pdb=" CB ILE D 46 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CG LEU B 236 " pdb=" CB LEU B 236 " pdb=" CD1 LEU B 236 " pdb=" CD2 LEU B 236 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 977 not shown) Planarity restraints: 1129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 234 " 0.061 5.00e-02 4.00e+02 9.20e-02 1.36e+01 pdb=" N PRO C 235 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO C 235 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 235 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 474 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" CD GLU A 474 " 0.047 2.00e-02 2.50e+03 pdb=" OE1 GLU A 474 " -0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU A 474 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 219 " 0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO C 220 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 220 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 220 " 0.030 5.00e-02 4.00e+02 ... (remaining 1126 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 169 2.69 - 3.24: 6035 3.24 - 3.80: 10359 3.80 - 4.35: 13735 4.35 - 4.90: 22943 Nonbonded interactions: 53241 Sorted by model distance: nonbonded pdb=" OD1 ASP C 72 " pdb=" N THR C 73 " model vdw 2.140 3.120 nonbonded pdb=" O LYS D 31 " pdb=" N VAL D 52 " model vdw 2.213 3.120 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.281 3.040 nonbonded pdb=" O VAL C 270 " pdb=" OG SER C 360 " model vdw 2.297 3.040 nonbonded pdb=" O HIS A 490 " pdb=" OG1 THR A 494 " model vdw 2.317 3.040 ... (remaining 53236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.020 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 6542 Z= 0.251 Angle : 0.872 11.564 8871 Z= 0.496 Chirality : 0.049 0.268 980 Planarity : 0.006 0.092 1129 Dihedral : 18.360 146.942 2440 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.02 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 24.46 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.29), residues: 796 helix: -0.01 (0.28), residues: 337 sheet: -0.66 (0.47), residues: 119 loop : -0.50 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 80 TYR 0.037 0.001 TYR A 475 PHE 0.019 0.001 PHE A 486 TRP 0.009 0.001 TRP C 128 HIS 0.005 0.001 HIS C 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.25 ( 6542) covalent geometry : angle 0.87211 / 0.50 ( 8871) hydrogen bonds : bond 0.16397 / 10.90 ( 284) hydrogen bonds : angle 6.64439 / 4.56 ( 783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.214 Fit side-chains REVERT: B 93 GLU cc_start: 0.6170 (mm-30) cc_final: 0.5755 (mm-30) REVERT: B 123 MET cc_start: 0.6936 (tpt) cc_final: 0.6735 (tpt) REVERT: B 161 HIS cc_start: 0.7348 (m90) cc_final: 0.6913 (m90) REVERT: B 210 ARG cc_start: 0.6301 (mtp-110) cc_final: 0.5977 (ttp-170) REVERT: B 211 ASP cc_start: 0.6754 (t0) cc_final: 0.6544 (t0) REVERT: B 269 MET cc_start: 0.7294 (mtp) cc_final: 0.7063 (mtt) REVERT: C 44 MET cc_start: 0.6002 (tmm) cc_final: 0.5633 (tpt) REVERT: C 68 THR cc_start: 0.6664 (m) cc_final: 0.6388 (t) REVERT: C 80 ARG cc_start: 0.7401 (ttm110) cc_final: 0.6767 (mtt90) REVERT: C 125 GLU cc_start: 0.7170 (pt0) cc_final: 0.6629 (pt0) REVERT: C 129 ASN cc_start: 0.7016 (p0) cc_final: 0.6296 (p0) REVERT: D 36 TRP cc_start: 0.7537 (m100) cc_final: 0.7329 (m100) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.5099 time to fit residues: 71.0605 Evaluate side-chains 113 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.0170 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS B 137 GLN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.165681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.156151 restraints weight = 8719.246| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.62 r_work: 0.3981 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6542 Z= 0.165 Angle : 0.651 7.960 8871 Z= 0.323 Chirality : 0.046 0.176 980 Planarity : 0.005 0.061 1129 Dihedral : 10.828 152.588 916 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.02 % Favored : 96.86 % Rotamer: Outliers : 4.63 % Allowed : 22.14 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.29), residues: 796 helix: 0.29 (0.28), residues: 350 sheet: -0.33 (0.46), residues: 121 loop : -0.34 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 80 TYR 0.016 0.002 TYR A 475 PHE 0.027 0.002 PHE A 486 TRP 0.011 0.002 TRP D 49 HIS 0.006 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 6542) covalent geometry : angle 0.65060 / 0.32 ( 8871) hydrogen bonds : bond 0.03448 / 2.26 ( 284) hydrogen bonds : angle 5.14117 / 3.50 ( 783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.252 Fit side-chains REVERT: B 137 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: B 151 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.7006 (tt) REVERT: B 297 THR cc_start: 0.8370 (m) cc_final: 0.8021 (p) REVERT: C 95 GLU cc_start: 0.6830 (tt0) cc_final: 0.6617 (tt0) REVERT: C 129 ASN cc_start: 0.7884 (p0) cc_final: 0.7063 (p0) REVERT: C 134 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7640 (mtp85) REVERT: C 177 HIS cc_start: 0.5089 (OUTLIER) cc_final: 0.4736 (m-70) REVERT: C 416 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7236 (mt-10) outliers start: 32 outliers final: 13 residues processed: 143 average time/residue: 0.4699 time to fit residues: 71.3161 Evaluate side-chains 129 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 177 HIS Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 416 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 35 optimal weight: 0.0670 chunk 66 optimal weight: 0.0170 chunk 46 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN B 137 GLN B 161 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS C 409 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.159734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.150280 restraints weight = 8603.329| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.54 r_work: 0.3934 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6542 Z= 0.140 Angle : 0.592 7.572 8871 Z= 0.293 Chirality : 0.045 0.157 980 Planarity : 0.004 0.048 1129 Dihedral : 10.061 146.638 916 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.14 % Favored : 96.73 % Rotamer: Outliers : 4.34 % Allowed : 22.87 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.29), residues: 796 helix: 0.59 (0.29), residues: 344 sheet: -0.17 (0.47), residues: 119 loop : -0.28 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 131 TYR 0.023 0.002 TYR A 475 PHE 0.024 0.002 PHE A 486 TRP 0.010 0.001 TRP C 395 HIS 0.004 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 6542) covalent geometry : angle 0.59186 / 0.29 ( 8871) hydrogen bonds : bond 0.03263 / 2.18 ( 284) hydrogen bonds : angle 4.97068 / 3.33 ( 783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.268 Fit side-chains REVERT: B 348 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7966 (m) REVERT: B 363 ASP cc_start: 0.7152 (m-30) cc_final: 0.6879 (m-30) REVERT: C 105 ASP cc_start: 0.7918 (m-30) cc_final: 0.7697 (m-30) REVERT: C 123 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8218 (mtt) REVERT: C 134 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7940 (mtm180) REVERT: C 141 MET cc_start: 0.7943 (mmm) cc_final: 0.7364 (mmm) REVERT: C 177 HIS cc_start: 0.5000 (OUTLIER) cc_final: 0.4653 (m90) REVERT: C 240 ARG cc_start: 0.7539 (tpp80) cc_final: 0.7278 (mtp-110) REVERT: C 401 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7877 (tt) outliers start: 30 outliers final: 14 residues processed: 147 average time/residue: 0.4589 time to fit residues: 71.7319 Evaluate side-chains 145 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 177 HIS Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 401 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.0870 chunk 50 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.0070 overall best weight: 0.2376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.160250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.150499 restraints weight = 8632.808| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.59 r_work: 0.3925 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6542 Z= 0.127 Angle : 0.568 7.367 8871 Z= 0.281 Chirality : 0.044 0.138 980 Planarity : 0.004 0.042 1129 Dihedral : 9.687 143.706 916 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.63 % Allowed : 23.44 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.30), residues: 796 helix: 0.84 (0.29), residues: 338 sheet: -0.12 (0.47), residues: 119 loop : -0.20 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 131 TYR 0.024 0.002 TYR A 475 PHE 0.024 0.001 PHE A 486 TRP 0.011 0.001 TRP B 356 HIS 0.003 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 6542) covalent geometry : angle 0.56849 / 0.28 ( 8871) hydrogen bonds : bond 0.03021 / 2.01 ( 284) hydrogen bonds : angle 4.87082 / 3.25 ( 783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.183 Fit side-chains REVERT: B 137 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7982 (mm110) REVERT: B 151 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7059 (tt) REVERT: B 348 SER cc_start: 0.8241 (OUTLIER) cc_final: 0.7986 (m) REVERT: B 363 ASP cc_start: 0.7270 (m-30) cc_final: 0.7007 (m-30) REVERT: C 105 ASP cc_start: 0.7892 (m-30) cc_final: 0.7668 (m-30) REVERT: C 108 TYR cc_start: 0.7551 (m-80) cc_final: 0.7224 (m-80) REVERT: C 134 ARG cc_start: 0.8232 (mtp180) cc_final: 0.7738 (mtp85) REVERT: C 177 HIS cc_start: 0.4937 (OUTLIER) cc_final: 0.4586 (m90) REVERT: C 240 ARG cc_start: 0.7497 (tpp80) cc_final: 0.7254 (mtp-110) REVERT: C 401 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7846 (tt) outliers start: 32 outliers final: 13 residues processed: 154 average time/residue: 0.5173 time to fit residues: 84.0482 Evaluate side-chains 136 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 177 HIS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 401 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 64 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 21 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.156451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.146611 restraints weight = 8523.334| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.57 r_work: 0.3867 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6542 Z= 0.210 Angle : 0.656 8.346 8871 Z= 0.327 Chirality : 0.047 0.190 980 Planarity : 0.005 0.042 1129 Dihedral : 9.651 142.361 916 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.49 % Allowed : 24.60 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.29), residues: 796 helix: 0.50 (0.29), residues: 340 sheet: -0.15 (0.46), residues: 121 loop : -0.16 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 25 TYR 0.024 0.002 TYR A 475 PHE 0.030 0.002 PHE A 486 TRP 0.015 0.002 TRP C 395 HIS 0.004 0.001 HIS C 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 ( 6542) covalent geometry : angle 0.65568 / 0.33 ( 8871) hydrogen bonds : bond 0.03571 / 2.37 ( 284) hydrogen bonds : angle 5.07646 / 3.42 ( 783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.281 Fit side-chains REVERT: B 151 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7284 (tt) REVERT: B 210 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6049 (ttp-170) REVERT: B 363 ASP cc_start: 0.7441 (m-30) cc_final: 0.7133 (m-30) REVERT: C 95 GLU cc_start: 0.6909 (tp30) cc_final: 0.6649 (tt0) REVERT: C 177 HIS cc_start: 0.5023 (OUTLIER) cc_final: 0.4493 (m90) REVERT: C 240 ARG cc_start: 0.7530 (tpp80) cc_final: 0.7291 (mtp-110) REVERT: C 245 PRO cc_start: 0.8162 (Cg_endo) cc_final: 0.7885 (Cg_exo) REVERT: C 401 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7904 (tt) outliers start: 31 outliers final: 14 residues processed: 153 average time/residue: 0.4872 time to fit residues: 78.9625 Evaluate side-chains 150 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 177 HIS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 401 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 19 optimal weight: 0.6980 chunk 40 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.155237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.145443 restraints weight = 8445.006| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.55 r_work: 0.3853 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6542 Z= 0.208 Angle : 0.660 8.498 8871 Z= 0.327 Chirality : 0.047 0.182 980 Planarity : 0.005 0.045 1129 Dihedral : 9.345 143.892 916 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.78 % Allowed : 25.33 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.29), residues: 796 helix: 0.43 (0.29), residues: 339 sheet: -0.17 (0.46), residues: 123 loop : -0.15 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 302 TYR 0.022 0.002 TYR A 475 PHE 0.032 0.002 PHE A 486 TRP 0.016 0.002 TRP C 395 HIS 0.004 0.001 HIS C 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 ( 6542) covalent geometry : angle 0.66045 / 0.33 ( 8871) hydrogen bonds : bond 0.03539 / 2.34 ( 284) hydrogen bonds : angle 5.05782 / 3.42 ( 783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.256 Fit side-chains REVERT: B 16 MET cc_start: 0.7222 (mtm) cc_final: 0.7013 (mtm) REVERT: B 151 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7340 (tt) REVERT: B 210 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.5918 (ttp-170) REVERT: C 93 MET cc_start: 0.8162 (mtm) cc_final: 0.7953 (mtm) REVERT: C 95 GLU cc_start: 0.6888 (tp30) cc_final: 0.6646 (tt0) REVERT: C 108 TYR cc_start: 0.7795 (m-80) cc_final: 0.7480 (m-80) REVERT: C 129 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7577 (p0) REVERT: C 169 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6301 (tt) REVERT: C 240 ARG cc_start: 0.7560 (tpp80) cc_final: 0.7314 (mtp-110) REVERT: C 245 PRO cc_start: 0.8196 (Cg_endo) cc_final: 0.7995 (Cg_exo) REVERT: C 401 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7905 (tt) outliers start: 33 outliers final: 17 residues processed: 154 average time/residue: 0.4653 time to fit residues: 75.9394 Evaluate side-chains 149 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 177 HIS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 401 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.154781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.144964 restraints weight = 8466.814| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.57 r_work: 0.3844 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6542 Z= 0.223 Angle : 0.682 9.751 8871 Z= 0.337 Chirality : 0.048 0.194 980 Planarity : 0.005 0.055 1129 Dihedral : 9.052 141.188 916 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.50 % Allowed : 25.62 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.29), residues: 796 helix: 0.35 (0.29), residues: 339 sheet: -0.27 (0.45), residues: 123 loop : -0.18 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 131 TYR 0.022 0.002 TYR A 475 PHE 0.031 0.002 PHE A 486 TRP 0.017 0.002 TRP C 395 HIS 0.004 0.001 HIS C 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.22 ( 6542) covalent geometry : angle 0.68240 / 0.34 ( 8871) hydrogen bonds : bond 0.03651 / 2.44 ( 284) hydrogen bonds : angle 5.08560 / 3.45 ( 783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.268 Fit side-chains REVERT: B 16 MET cc_start: 0.7216 (mtm) cc_final: 0.6983 (mtm) REVERT: B 151 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7442 (tt) REVERT: B 210 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.5893 (ttp-170) REVERT: C 95 GLU cc_start: 0.6896 (tp30) cc_final: 0.6640 (tt0) REVERT: C 169 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6278 (tt) REVERT: C 240 ARG cc_start: 0.7608 (tpp80) cc_final: 0.7359 (mtp-110) REVERT: C 245 PRO cc_start: 0.8213 (Cg_endo) cc_final: 0.7954 (Cg_exo) REVERT: C 307 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.5878 (mm-30) REVERT: C 401 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7875 (tt) outliers start: 38 outliers final: 19 residues processed: 151 average time/residue: 0.4790 time to fit residues: 76.6818 Evaluate side-chains 144 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 177 HIS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 401 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 0.0010 chunk 26 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 0.0170 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.156699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.146920 restraints weight = 8467.073| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.57 r_work: 0.3870 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6542 Z= 0.142 Angle : 0.622 9.953 8871 Z= 0.305 Chirality : 0.044 0.134 980 Planarity : 0.005 0.047 1129 Dihedral : 8.463 133.233 916 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.33 % Allowed : 28.22 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.30), residues: 796 helix: 0.66 (0.29), residues: 339 sheet: -0.25 (0.45), residues: 121 loop : -0.03 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 427 TYR 0.022 0.002 TYR C 417 PHE 0.023 0.002 PHE A 486 TRP 0.013 0.001 TRP B 356 HIS 0.002 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 6542) covalent geometry : angle 0.62155 / 0.31 ( 8871) hydrogen bonds : bond 0.03168 / 2.11 ( 284) hydrogen bonds : angle 4.88444 / 3.28 ( 783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.247 Fit side-chains REVERT: B 16 MET cc_start: 0.7119 (mtm) cc_final: 0.6893 (mtm) REVERT: B 151 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7357 (tt) REVERT: C 108 TYR cc_start: 0.7761 (m-80) cc_final: 0.7489 (m-80) REVERT: C 123 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8324 (mtt) REVERT: C 129 ASN cc_start: 0.7812 (t0) cc_final: 0.7464 (t0) REVERT: C 240 ARG cc_start: 0.7482 (tpp80) cc_final: 0.7260 (mtp-110) REVERT: C 245 PRO cc_start: 0.8209 (Cg_endo) cc_final: 0.7995 (Cg_exo) REVERT: C 384 ASN cc_start: 0.7854 (p0) cc_final: 0.7573 (p0) REVERT: C 401 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7842 (tt) outliers start: 23 outliers final: 16 residues processed: 155 average time/residue: 0.4701 time to fit residues: 77.1803 Evaluate side-chains 150 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 401 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 0.0970 chunk 54 optimal weight: 0.5980 chunk 59 optimal weight: 0.0040 chunk 77 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 79 optimal weight: 0.5980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 163 ASN C 355 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.157908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.148150 restraints weight = 8515.237| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.55 r_work: 0.3873 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6542 Z= 0.145 Angle : 0.620 9.551 8871 Z= 0.307 Chirality : 0.045 0.154 980 Planarity : 0.005 0.047 1129 Dihedral : 8.034 125.404 916 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.89 % Allowed : 29.52 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.30), residues: 796 helix: 0.73 (0.29), residues: 339 sheet: -0.08 (0.45), residues: 117 loop : 0.02 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 427 TYR 0.021 0.002 TYR C 417 PHE 0.024 0.002 PHE A 486 TRP 0.014 0.001 TRP C 128 HIS 0.003 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 6542) covalent geometry : angle 0.62045 / 0.31 ( 8871) hydrogen bonds : bond 0.03165 / 2.12 ( 284) hydrogen bonds : angle 4.87312 / 3.27 ( 783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.288 Fit side-chains REVERT: B 16 MET cc_start: 0.7053 (mtm) cc_final: 0.6837 (mtm) REVERT: B 151 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7369 (tt) REVERT: B 325 MET cc_start: 0.6593 (ttm) cc_final: 0.6321 (ttp) REVERT: C 108 TYR cc_start: 0.7764 (m-80) cc_final: 0.7494 (m-80) REVERT: C 240 ARG cc_start: 0.7464 (tpp80) cc_final: 0.7241 (mtp-110) REVERT: C 245 PRO cc_start: 0.8215 (Cg_endo) cc_final: 0.7978 (Cg_exo) REVERT: C 401 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7887 (tt) outliers start: 20 outliers final: 14 residues processed: 136 average time/residue: 0.4351 time to fit residues: 62.8581 Evaluate side-chains 141 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 401 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 69 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.157365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.147649 restraints weight = 8464.340| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.54 r_work: 0.3867 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6542 Z= 0.174 Angle : 0.646 8.888 8871 Z= 0.319 Chirality : 0.046 0.155 980 Planarity : 0.005 0.047 1129 Dihedral : 7.860 121.379 916 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.18 % Allowed : 29.23 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.29), residues: 796 helix: 0.74 (0.29), residues: 333 sheet: -0.14 (0.45), residues: 117 loop : -0.04 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 427 TYR 0.021 0.002 TYR A 475 PHE 0.027 0.002 PHE A 486 TRP 0.015 0.002 TRP C 395 HIS 0.004 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 ( 6542) covalent geometry : angle 0.64574 / 0.32 ( 8871) hydrogen bonds : bond 0.03329 / 2.21 ( 284) hydrogen bonds : angle 4.95116 / 3.32 ( 783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.192 Fit side-chains REVERT: B 151 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7403 (tt) REVERT: C 108 TYR cc_start: 0.7799 (m-80) cc_final: 0.7523 (m-80) REVERT: C 240 ARG cc_start: 0.7486 (tpp80) cc_final: 0.7259 (mtp-110) REVERT: C 245 PRO cc_start: 0.8220 (Cg_endo) cc_final: 0.8014 (Cg_exo) REVERT: C 401 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7840 (tt) outliers start: 22 outliers final: 17 residues processed: 138 average time/residue: 0.4098 time to fit residues: 60.1650 Evaluate side-chains 140 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 401 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 26 optimal weight: 0.2980 chunk 11 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 43 optimal weight: 0.0870 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.157825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.148212 restraints weight = 8499.952| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 1.53 r_work: 0.3870 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6542 Z= 0.152 Angle : 0.614 9.070 8871 Z= 0.306 Chirality : 0.045 0.145 980 Planarity : 0.005 0.048 1129 Dihedral : 7.606 115.847 916 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.33 % Allowed : 29.96 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.30), residues: 796 helix: 0.84 (0.29), residues: 333 sheet: -0.13 (0.45), residues: 117 loop : 0.00 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 427 TYR 0.020 0.002 TYR A 475 PHE 0.024 0.002 PHE A 486 TRP 0.014 0.002 TRP C 128 HIS 0.003 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 6542) covalent geometry : angle 0.61370 / 0.31 ( 8871) hydrogen bonds : bond 0.03147 / 2.09 ( 284) hydrogen bonds : angle 4.88025 / 3.27 ( 783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2584.57 seconds wall clock time: 45 minutes 7.84 seconds (2707.84 seconds total)